LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-739-g2644e7f6fa-modified)
  using 1 OpenMP thread(s) per MPI task

units           real

atom_style      full
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic

pair_style      lj/charmm/coul/long 8 10
pair_modify     mix arithmetic
kspace_style    pppm 1e-4

read_data       data.bpti
Reading data file ...
  orthogonal box = (-10 -10 -30) to (50 50 30)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  892 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  18 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  orthogonal box = (-10 -10 -30) to (50 50 30)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  906 bonds
  reading angles ...
  1626 angles
  reading dihedrals ...
  2501 dihedrals
  reading impropers ...
  137 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     9 = max # of 1-3 neighbors
    19 = max # of 1-4 neighbors
    21 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.016 seconds

special_bonds   charmm
neigh_modify    delay 2 every 1


# ------------- MINIMIZE ----------

minimize 	1e-4 1e-6 1000 10000
Switching to 'neigh_modify every 1 delay 0 check yes' setting during minimization
PPPM initialization ...
WARNING: System is not charge neutral, net charge = 6
For more information see https://docs.lammps.org/err0029 (src/kspace.cpp:330)
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.20327216
  grid = 16 16 16
  stencil order = 5
  estimated absolute RMS force accuracy = 0.031639896
  estimated relative force accuracy = 9.5282607e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 9261 4096
Generated 378 of 378 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 10 10 10
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 18.22 | 18.22 | 18.22 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0             -3075.6497      943.91164     -2131.7381     -380.67775    
       241   0             -4503.3151      749.58684     -3753.7283     -29.038816    
Loop time of 1.09677 on 1 procs for 241 steps with 892 atoms

99.5% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final = 
     -2131.73809529935  -3753.44164665875  -3753.72825893915
  Force two-norm initial, final = 1086.2055 26.365941
  Force max component initial, final = 310.81136 3.9384524
  Final line search alpha, max atom move = 0.0059668226 0.023500047
  Iterations, force evaluations = 241 463

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.85894    | 0.85894    | 0.85894    |   0.0 | 78.32
Bond    | 0.059945   | 0.059945   | 0.059945   |   0.0 |  5.47
Kspace  | 0.14876    | 0.14876    | 0.14876    |   0.0 | 13.56
Neigh   | 0.024436   | 0.024436   | 0.024436   |   0.0 |  2.23
Comm    | 0.00021908 | 0.00021908 | 0.00021908 |   0.0 |  0.02
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.004464   |            |       |  0.41

Nlocal:            892 ave         892 max         892 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             31 ave          31 max          31 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         148892 ave      148892 max      148892 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 148892
Ave neighs/atom = 166.91928
Ave special neighs/atom = 10.939462
Neighbor list builds = 15
Dangerous builds = 0
reset_timestep  0

# ------------- RUN ---------------

thermo          100
thermo_style    multi
timestep	8

run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
Respa levels:
  1 = bond angle
  2 = dihedral improper pair
  3 = kspace

velocity        all create 200.0 12345678 dist uniform
#dump            dump1 all atom 100 4pti.dump

fix             1 all nvt temp 200 300 25
fix             cor all filter/corotate m 1.0
  163 = # of size 2 clusters
  0 = # of size 3 clusters
  25 = # of size 4 clusters
  0 = # of size 5 clusters
  100 = # of frozen angles

run             1000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- Mollified Impulse Method with Corotational Filter: doi:10.1016/j.jcp.2016.12.024

@Article{Fath2017,
 Title ={A Fast Mollified Impulse Method for Biomolecular Atomistic Simulations},
 Author = {L. Fath and M. Hochbruck and C. V. Singh},
 Journal = {Journal of Computational Physics},
 Year = {2017},
 Pages = {180--198},
 Volume = {333},

 Doi = {https://doi.org/10.1016/j.jcp.2016.12.024},
 ISSN = {0021-9991},
 Keywords = {Mollified impulse method},
 Url = {https://www.sciencedirect.com/science/article/pii/S0021999116306787}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.20327216
  grid = 16 16 16
  stencil order = 5
  estimated absolute RMS force accuracy = 0.031639896
  estimated relative force accuracy = 9.5282607e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 9261 4096
Generated 378 of 378 mixed pair_coeff terms from arithmetic mixing rule
Per MPI rank memory allocation (min/avg/max) = 19.9 | 19.9 | 19.9 Mbytes
------------ Step              0 ----- CPU =            0 (sec) -------------
TotEng   =     -3220.3397 KinEng   =       531.1804 Temp     =       200.0000 
PotEng   =     -3751.5200 E_bond   =        42.2799 E_angle  =       345.2600 
E_dihed  =       337.8366 E_impro  =        24.2104 E_vdwl   =      -288.5348 
E_coul   =      -886.3627 E_long   =     -3326.2093 Press    =        83.2346
------------ Step            100 ----- CPU =     1.302865 (sec) -------------
TotEng   =     -2718.4639 KinEng   =       539.6162 Temp     =       203.1763 
PotEng   =     -3258.0801 E_bond   =       203.2240 E_angle  =       566.1699 
E_dihed  =       397.6784 E_impro  =        34.7677 E_vdwl   =      -248.6455 
E_coul   =      -874.8598 E_long   =     -3336.4148 Press    =       135.8491
------------ Step            200 ----- CPU =     2.621053 (sec) -------------
TotEng   =     -2665.8734 KinEng   =       622.6154 Temp     =       234.4271 
PotEng   =     -3288.4888 E_bond   =       207.6877 E_angle  =       590.1136 
E_dihed  =       389.1793 E_impro  =        30.5643 E_vdwl   =      -240.8931 
E_coul   =      -926.1769 E_long   =     -3338.9637 Press    =       103.1349
------------ Step            300 ----- CPU =     3.933001 (sec) -------------
TotEng   =     -2669.8848 KinEng   =       617.4017 Temp     =       232.4641 
PotEng   =     -3287.2866 E_bond   =       202.1536 E_angle  =       570.7734 
E_dihed  =       382.5535 E_impro  =        41.1356 E_vdwl   =      -220.7740 
E_coul   =      -921.3674 E_long   =     -3341.7612 Press    =        45.4258
------------ Step            400 ----- CPU =     5.256403 (sec) -------------
TotEng   =     -2598.0952 KinEng   =       663.8358 Temp     =       249.9474 
PotEng   =     -3261.9310 E_bond   =       200.1728 E_angle  =       621.6410 
E_dihed  =       405.7274 E_impro  =        42.3035 E_vdwl   =      -220.9709 
E_coul   =      -965.7808 E_long   =     -3345.0240 Press    =       -94.9231
------------ Step            500 ----- CPU =     6.594295 (sec) -------------
TotEng   =     -2539.6839 KinEng   =       691.7313 Temp     =       260.4506 
PotEng   =     -3231.4152 E_bond   =       248.6516 E_angle  =       599.5593 
E_dihed  =       407.3768 E_impro  =        41.6863 E_vdwl   =      -208.6839 
E_coul   =      -980.1790 E_long   =     -3339.8263 Press    =       124.6829
------------ Step            600 ----- CPU =     7.940297 (sec) -------------
TotEng   =     -2537.9670 KinEng   =       685.2804 Temp     =       258.0217 
PotEng   =     -3223.2474 E_bond   =       238.2834 E_angle  =       650.7806 
E_dihed  =       409.9036 E_impro  =        44.8168 E_vdwl   =      -216.9781 
E_coul   =     -1014.1330 E_long   =     -3335.9207 Press    =         7.8957
------------ Step            700 ----- CPU =     9.271543 (sec) -------------
TotEng   =     -2480.5039 KinEng   =       714.5391 Temp     =       269.0382 
PotEng   =     -3195.0430 E_bond   =       259.0199 E_angle  =       640.4605 
E_dihed  =       402.0797 E_impro  =        45.4797 E_vdwl   =      -222.0960 
E_coul   =      -979.2502 E_long   =     -3340.7366 Press    =       -24.9541
------------ Step            800 ----- CPU =     10.60394 (sec) -------------
TotEng   =     -2486.4077 KinEng   =       745.7774 Temp     =       280.8001 
PotEng   =     -3232.1852 E_bond   =       228.4920 E_angle  =       661.2193 
E_dihed  =       393.2993 E_impro  =        41.1393 E_vdwl   =      -229.2836 
E_coul   =      -990.3347 E_long   =     -3336.7167 Press    =        17.0072
------------ Step            900 ----- CPU =     11.94578 (sec) -------------
TotEng   =     -2432.8868 KinEng   =       768.7365 Temp     =       289.4446 
PotEng   =     -3201.6233 E_bond   =       245.9573 E_angle  =       641.2719 
E_dihed  =       405.4804 E_impro  =        45.7278 E_vdwl   =      -222.1212 
E_coul   =      -978.2677 E_long   =     -3339.6718 Press    =        -0.8352
------------ Step           1000 ----- CPU =     13.26214 (sec) -------------
TotEng   =     -2379.5373 KinEng   =       769.6457 Temp     =       289.7870 
PotEng   =     -3149.1830 E_bond   =       267.3657 E_angle  =       680.2194 
E_dihed  =       394.4674 E_impro  =        46.3983 E_vdwl   =      -180.6283 
E_coul   =     -1019.0133 E_long   =     -3337.9922 Press    =       197.8529
Loop time of 13.2622 on 1 procs for 1000 steps with 892 atoms

Performance: 52.118 ns/day, 0.460 hours/ns, 75.403 timesteps/s, 67.259 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 11.019     | 11.019     | 11.019     |   0.0 | 83.08
Bond    | 1.3404     | 1.3404     | 1.3404     |   0.0 | 10.11
Kspace  | 0.31706    | 0.31706    | 0.31706    |   0.0 |  2.39
Neigh   | 0.31121    | 0.31121    | 0.31121    |   0.0 |  2.35
Comm    | 0.0047645  | 0.0047645  | 0.0047645  |   0.0 |  0.04
Output  | 0.00027548 | 0.00027548 | 0.00027548 |   0.0 |  0.00
Modify  | 0.23486    | 0.23486    | 0.23486    |   0.0 |  1.77
Other   |            | 0.03482    |            |       |  0.26

Nlocal:            892 ave         892 max         892 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             31 ave          31 max          31 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         145768 ave      145768 max      145768 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 145768
Ave neighs/atom = 163.41704
Ave special neighs/atom = 10.939462
Neighbor list builds = 190
Dangerous builds = 0

unfix           cor
unfix           1

Total wall time: 0:00:14
